Twilight princess seems to be more less of a issue then the other two. In TP, everything is nice and smooth up intill I reach Ordon Village. From there it drops to around 25 FPS. TP works best for me using OpenGL as backend. The other two have no chance of running OpenGL as backend for whatever reason. Xenoblade (DX11) seems all fine up intill the tutorial battle. Last story(DX11) happens right at the starting and cant get any good FPS.

I've tried almost all combinations of settings to get the games working better. None seem to really improve the slow down issues. I've checked the wiki for said games and doing the fixes/gfx enhance don't seem to improve speed. I really don't know how to solve this as this is a new computer. Any help would be wonderful.

Try to OC your CPU.
I have FX 4300 @ 4400MHz - Xenoblade runs at fullspeed 90% of time. The Last Story is playable (at least for me, I've finished Metroid Prime on my old system with ~60% speed and ~30% speed on major endgame battles. Yeah, I'm kinda masochistic )